Contacts of the helix formed by residues 413 - 425 (chain L) in PDB entry 1KYO
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 413 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362L VAL* 4.6 4.5 - - - -
411L ALA 3.4 14.8 - - - +
412L ILE* 1.3 75.4 - - - +
414L VAL* 1.3 67.8 + - - +
415L LYS* 3.7 12.2 + - - +
416L ASP* 2.9 41.7 + - - +
417L VAL* 3.2 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 414 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357L VAL* 3.6 22.0 - - + +
358L THR 3.9 2.2 - - - +
359L ASP* 3.6 47.8 - - - +
362L VAL* 3.8 23.1 - - + +
413L THR* 1.3 72.2 - - - +
415L LYS* 1.3 65.5 + - - +
417L VAL* 3.0 16.0 + - - +
418L LYS* 3.2 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 415 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413L THR* 3.7 11.4 - - - +
414L VAL* 1.3 83.3 - - - +
416L ASP* 1.3 60.7 + - - +
418L LYS* 3.5 11.5 + - + +
419L ALA* 3.3 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 416 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273L ASN* 5.7 0.7 + - - -
276L VAL* 4.0 14.7 - - + +
411L ALA 4.2 2.9 - - - +
412L ILE* 3.5 18.4 - - + +
413L THR* 2.9 36.2 + - - +
415L LYS* 1.3 76.6 - - - +
417L VAL* 1.3 64.7 + - - +
419L ALA* 3.3 7.2 + - - +
420L TRP* 3.2 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 417 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276L VAL* 4.0 12.6 - - + +
279L LEU* 3.7 29.8 - - + -
280L ALA* 4.7 11.0 - - + -
283L ILE* 4.6 6.3 - - + -
353L LEU* 3.8 33.2 - - + -
357L VAL* 4.4 9.9 - - + -
362L VAL* 4.1 11.7 - - + -
412L ILE* 4.2 6.1 - - + -
413L THR 3.7 11.4 - - - +
414L VAL 3.0 7.1 + - - +
416L ASP* 1.3 75.9 - - - +
418L LYS* 1.3 57.7 - - - +
420L TRP* 3.5 3.5 + - + +
421L ALA* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 418 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353L LEU 3.1 20.3 - - - +
354L THR* 3.9 20.7 - - - +
355L ILE 3.3 25.7 + - - -
356L SER* 4.8 1.0 - - - +
357L VAL* 4.1 17.8 + - + +
414L VAL* 3.2 33.5 + - + +
415L LYS* 3.7 11.7 - - + +
417L VAL* 1.3 74.8 - - - +
419L ALA* 1.3 59.9 + - - +
421L ALA* 3.4 1.7 + - - +
422L GLY* 2.8 26.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 419 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415L LYS 3.3 9.8 + - - +
416L ASP* 3.3 10.0 + - - +
418L LYS* 1.3 76.7 - - - +
420L TRP* 1.3 63.8 + - - +
422L GLY* 3.0 11.2 + - - -
423L LYS* 3.1 22.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 420 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266L GLY* 5.7 0.7 - - - -
267L GLU* 3.2 38.1 + - + +
273L ASN* 3.6 23.6 - - + +
276L VAL* 3.8 15.7 - - + -
277L ALA* 3.5 24.0 - - + +
280L ALA* 3.6 25.6 - - + -
327L TRP* 3.1 45.5 - + + -
353L LEU* 4.5 2.5 - - + -
416L ASP 3.2 10.6 + - - +
417L VAL* 3.6 10.8 - - + +
419L ALA* 1.3 80.1 - - - +
421L ALA* 1.3 72.0 + - + +
423L LYS* 3.3 4.2 + - - +
424L ARG* 2.8 55.3 + - + +
425L LEU* 4.2 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 421 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353L LEU* 3.4 34.3 - - + +
354L THR* 3.5 12.8 - - - +
417L VAL 2.9 18.5 + - - +
418L LYS 3.7 0.9 - - - +
420L TRP* 1.3 88.8 - - + +
422L GLY* 1.3 57.6 + - - +
425L LEU* 2.8 33.1 + - + -
426L TRP 2.8 13.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 422 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354L THR* 3.9 9.4 + - - -
418L LYS 2.8 16.2 + - - -
419L ALA* 3.0 5.5 + - - -
421L ALA* 1.3 77.9 - - - +
423L LYS* 1.3 62.8 + - - +
426L TRP* 3.9 23.4 - - - +
13T ARG* 3.9 12.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 423 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419L ALA* 3.1 15.3 + - + +
420L TRP* 3.7 7.6 - - - +
422L GLY* 1.3 79.0 - - - +
424L ARG* 1.3 78.9 + - - +
425L LEU 3.7 0.2 - - - -
428L GLN* 3.4 13.5 + - - +
13T ARG* 3.4 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 424 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264L VAL* 3.6 18.6 - - + +
265L GLU* 3.6 41.8 + - - +
266L GLY 2.9 24.3 + - - +
267L GLU* 3.0 36.5 + - + +
268L PRO* 5.0 4.2 - - - +
420L TRP* 2.8 50.8 + - + +
423L LYS* 1.3 88.0 + - - +
425L LEU* 1.3 58.4 + - - +
428L GLN* 3.4 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 425 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264L VAL* 3.6 35.2 - - + -
327L TRP* 3.5 42.4 - - + -
350L TRP* 4.0 21.3 - - + +
353L LEU* 3.8 19.5 - - + -
354L THR* 5.1 0.7 - - - +
420L TRP* 4.2 10.1 - - + -
421L ALA* 2.8 23.9 + - + +
424L ARG* 1.3 75.5 - - + +
426L TRP* 1.3 63.9 + - - +
427L ASP 3.2 3.3 + - - -
428L GLN* 3.5 9.8 + - - +
451L MET* 3.2 31.4 - - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il